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Series GSE186381 Query DataSets for GSE186381
Status Public on Oct 01, 2023
Title Methylation analysis of serum cfDNA pooled samples for the discovery of non-invasive biomarkers for colorectal cancer
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary We explored the differential methylation patterns found in cfDNA between no neoplasia (NN; individuals with no colorectal findings, benign pathologies and non-advanced adenomas) and patients with advanced neoplasia (AN; advanced adenomas and colorectal cancer) using pooled samples, for the discovery of non-invasive methylation biomarkers for CRC screening. cfDNA was extracted from serum samples and methylation measurements were assessed with the Infinium MethylationEPIC BeadChip. Data was mainly preprocessed and analyzed with R/Bioconductor packages.
 
Overall design We explored the differential methylation patterns found in cfDNA between no neoplasia and advanced neoplasia using pooled samples.
cfDNA was extracted from 280 serum samples with a modifed phenol-chlorophorm protocol. A total of 28 cfDNA pooled samples were constructed using equal amounts of cfDNA from 5 men and 5 women with the same colorectal pathology as described in Gallardo-Gómez et al., Clinical Epigenetics 2018;10:53 (PMID: 29686738). cfDNA was bisulfite treated and was analyzed with the Infinium MethylationEPIC BeadChip microarray, covering over 850,000 CpG sites across the genome.
 
Contributor(s) Gallardo-Gómez M, De Chiara L
Citation(s) 37794510
Submission date Oct 22, 2021
Last update date Oct 18, 2023
Contact name María Gallardo-Gómez
E-mail(s) mgallardo@uvigo.es
Organization name Universidad de Vigo
Street address Campus As Lagoas Marcosende
City Vigo
ZIP/Postal code 36310
Country Spain
 
Platforms (1)
GPL21145 Infinium MethylationEPIC
Samples (28)
GSM5646628 No colorectal findings cfDNA pool A1
GSM5646629 Benign pathologies cfDNA pool A2
GSM5646630 Non-advanced adenomas cfDNA pool A3
Relations
BioProject PRJNA773710

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE186381_RAW.tar 161.2 Mb (http)(custom) TAR
GSE186381_signal_intensities.txt.gz 396.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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